GapMind for catabolism of small carbon sources

 

L-valine catabolism in Geobacter daltonii FRC-32

Best path

livF, livG, livJ, livH, livM, vorA*, vorB, vorC, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small

Rules

Overview: Valine degradation in GapMind is based on MetaCyc pathway L-valine degradation I (link). The other pathways do not produce any fixed carbon and are not included.

47 steps (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-valine ABC transporter, ATPase component 1 (LivF/BraG) GEOB_RS13900 GEOB_RS11345
livG L-valine ABC transporter, ATPase component 2 (LivG/BraF) GEOB_RS13895 GEOB_RS08235
livJ L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) GEOB_RS13880
livH L-valine ABC transporter, permease component 1 (LivH/BraD) GEOB_RS13885
livM L-valine ABC transporter, permease component 2 (LivM/BraE) GEOB_RS13890
vorA* branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA GEOB_RS14910 with GEOB_RS14905
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB GEOB_RS14915 GEOB_RS13225
vorC branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
acdH isobutyryl-CoA dehydrogenase GEOB_RS10880 GEOB_RS10900
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase GEOB_RS00800 GEOB_RS01210
bch 3-hydroxyisobutyryl-CoA hydrolase GEOB_RS12040 GEOB_RS01210
mmsB 3-hydroxyisobutyrate dehydrogenase
mmsA methylmalonate-semialdehyde dehydrogenase GEOB_RS17645 GEOB_RS12935
pccA propionyl-CoA carboxylase, alpha subunit GEOB_RS15185 GEOB_RS17375
pccB propionyl-CoA carboxylase, beta subunit GEOB_RS04165
epi methylmalonyl-CoA epimerase GEOB_RS04185
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit GEOB_RS04180
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit GEOB_RS15605
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase GEOB_RS13180
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
Bap2 L-valine permease Bap2
bcaP L-valine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit GEOB_RS09725
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit GEOB_RS09730 GEOB_RS06820
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component GEOB_RS09735 GEOB_RS09710
brnQ L-valine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase
hpcD 3-hydroxypropionyl-CoA dehydratase GEOB_RS01210 GEOB_RS15615
iolA malonate semialdehyde dehydrogenase (CoA-acylating) GEOB_RS17645 GEOB_RS12935
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component GEOB_RS09715 GEOB_RS04985
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components GEOB_RS04180
natA L-valine ABC transporter, ATPase component 1 (NatA) GEOB_RS13895 GEOB_RS13900
natB L-valine ABC transporter, substrate-binding component NatB
natC L-valine ABC transporter, permease component 1 (NatC)
natD L-valine ABC transporter, permease component 2 (NatD)
natE L-valine ABC transporter, ATPase component 2 (NatE) GEOB_RS13900 GEOB_RS11345
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA GEOB_RS13225
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB GEOB_RS13230
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit GEOB_RS15185 GEOB_RS17375
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase GEOB_RS11170
phtJ L-valine uptake permease PhtJ
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase GEOB_RS17655 GEOB_RS02545
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory